Tuesday, 25 April 2017

A great paper HERE that uses genomic analysis to understand the large phenotypic variability observed in 160 breeds of modern dogs.

The abstract:

There are nearly 400 modern domestic dog breeds with a unique histories and genetic profiles. To track the genetic signatures of breed development, we have assembled the most diverse dataset of dog. breeds, reflecting their extensive phenotypic variation and heritage. Combining genetic distance, migration, and genome-wide haplotype sharing analyses, we uncover geographic patterns of development and independent origins of common traits. Our analyses reveal the hybrid history of breeds and elucidate the effects of immigration, revealing for the first time a suggestion of New World dog within some modern breeds. Finally, we used cladistics and haplotype sharing to show that some common traits have arisen more than once in the history of the dog. These analyses characterize the complexities of breed development, resolving longstanding questions regarding individual breed origination, the effect of migration on geographically distinct breeds, and, by inference, transfer of trait and disease alleles among dog breeds.

Normal human vision is an unbelievably complex and sophisticated thing. Here is a special issue of Vision Research on one tiny component of vision - fixational eye movements and perception:

During viewing of a stationary scene, rapid gaze shifts, known as
saccades, occur every few hundreds of milliseconds. Saccades separate
fixations, the periods of apparent eye immobility in which visual
information is acquired and processed. Close inspection of oculomotor
activity in these periods reveals, however, that the very world
“fixation” is misleading: small eye movements incessantly occur in the
inter-saccadic intervals, suggesting an even deeper coupling between
visual functions and oculomotor activity. These gaze shifts come in
different varieties and are collectively known as fixational eye
movements. Although humans are normally not aware of making them, they
displace the retinal image at speeds that would be clearly visible had
the motion originated from the visual scene rather than the observer.

I don't know of any other human occupation, even including what I have seen of art, in which the people engaged in it are so caught up, so totally preoccupied, so driven beyond their strength and resources.

Scientists at work have the look of creatures following genetic instructions; they seem to be under the influence of a deeply placed human instinct. They are, despite their efforts at dignity, rather like young animals engaged in savage play. When they are near to an answer their hair stands on end, they sweat, they are awash in their own adrenalin. To grab the answer, and grab it first, is for them a more powerful drive than feeding or breeding or protecting themselves against the elements.

It sometimes looks like a lonely activity, but it is as much the opposite of lonely as human behavior can be. There is nothing so social, so communal, and so interdependent. An active field of science is like an immense intellectual anthill; the individual almost vanishes into the mass of minds tumbling over each other, carrying information from place to place, passing it around at the speed of light.

There are special kinds of information that seem to be chemotactic. As soon as a trace is released, receptors at the back of the neck are caused to tremble, there is a massive convergence of motile minds flying upwind on a gradient of surprise, crowding around the source. It is an infiltration of intellects, an inflammation.

There is nothing to touch the spectacle. In the midst of what seems a collective derangement of minds in total disorder, with bits of information being scattered about, torn to shreds, disintegrated, deconstituted, engulfed, in a kind of activity that seems as random and agitated as that of bees in a disturbed part of the hive, there suddenly emerges, with the purity of a slow phrase of music, a single new piece of truth about nature.

In short, it works. It is the most powerful and productive of the things human beings have learned to do together in many centuries, more effective than farming, or hunting and fishing, or building cathedrals, or making money. It is instinctive behavior, in my view, and I do not understand how it works.

It cannot be prearranged in any precise way; the minds cannot be lined up in tidy rows and given directions from printed sheets. You cannot get it done by instructing each mind to make this or that piece, for central committees to fit with the pieces made by the other instructed minds. It does not work this way.

What it needs is for the air to be made right. If you want a bee to make honey, you do not issue protocols on solar navigation or carbohydrate chemistry, you put him together with other bees (and you'd better do this quickly, for solitary bees do not stay alive) and you do what you can to arrange the general environment around the hive. If the air is right, the science will come in its own season, like pure honey.

Thursday, 20 April 2017

Many members of the British public will be under the impression that the billions of pounds of their taxes that are spent every year by UK Government agencies on biomedical science, is money well spent. Apparently, the reality is in fact quite the opposite.

HERE is a frankly shocking editorial by Dr Richard Horton Fellow of the Royal College of Physicians, the 55 year old Editor of The Lancet, one of the world's top medical journals.

In this piece, Horton describes a cosy meeting held under the Chatham House rule at the Wellcome Trust in April 2015 with some of the UK's top funders of biomedical science; the BBSRC, the MRC and the Wellcome Trust.

Two of these agencies are handsomely paid for by the UK Government, with the aim of funding the highest quality basic biomedical science. In 2015/2016 the BBSRC spent £473 Million and the MRC £927.8 Million. Every penny of which was derived from UK tax payers.

The case against science is straightforward: much of the scientific literature, perhaps half, may simply be untrue. Afflicted by studies with small sample sizes, tiny effects, invalid exploratory analyses, and flagrant conflicts of interest, together with an obsession for pursuing fashionable trends of dubious importance, science has taken a turn towards darkness. As one participant put it, “poor methods get results”. The Academy of Medical Sciences, Medical Research Council, and Biotechnology and Biological Sciences Research Council have now put their reputational weight behind an investigation into these questionable research practices. The apparent endemicity of bad research behaviour is alarming. In their quest for telling a compelling story, scientists too often sculpt data to fit their preferred theory of the world. Or they retrofit hypotheses to fit their data. Journal editors deserve their fair share of criticism too. We aid and abet the worst behaviours. Our acquiescence to the impact factor fuels an unhealthy competition to win a place in a select few journals. Our love of “significance” pollutes the literature with many a statistical fairy-tale. We reject important confirmations. Journals are not the only miscreants. Universities are in a perpetual struggle for money and talent, endpoints that foster reductive metrics, such as high-impact publication. National assessment procedures,such as the Research Excellence Framework, incentivise bad practices. And individual scientists, including their most senior leaders, do little to alter a research culture that occasionally veers close to misconduct.

Dr Horton then goes on to say:

Can bad scientific practices be fixed? Part of the problem is that no-one is incentivised to be right. Instead, scientists are incentivised to be productive and innovative.

This is shameful. No scientist should need to be incentivised to be right. Science, if it is anything at all, is all about being right. Meaning in this case: seeking to understand the truth about nature and natural phenomena.

The sponsors of the symposium that Horton attended in April 2015 have published the outcomes of the symposium, an action plan and an update on progress HERE. Perhaps, in years to come, the next editor of The Lancet may be able to write an opinion piece which describes a situation in bio medical science that is very different than today's: A turn away from darkness.

Tuesday, 18 April 2017

Sunday, 16 April 2017

The conclusions reached in science are always, when looked at closely,
far more provisional and tentative than are most of the assumptions
arrived at by our colleagues in the humanities. But we do not talk much
in public about this, nor do we teach this side of science. We tend to
say instead: These are the facts of the matter, and this is what the
facts signify. Go and learn them, for they will be the same forever.

Saturday, 15 April 2017

Here is a superb paper from 1958 by Bernard Barber and Renée C. Fox; The Case of the Floppy-Eared Rabbits: An Instance of Serendipity Gained and Serendipity Lost.

ABSTRACT

Twodistinguished medical scientists independently observed the same phenomenon in the course of their research: reversible collapse of rabbits' ears after injection of the enzyme papain. One went on to make a discovery based on this serendipitous or chance occurrence; the other did not. Intensive tandem interviews were conducted with each of these scientists in order to discover similarities and differences in their experiences with the floppy-eared rabbits. These interview materials are analyzed for the light they shed on the process of scientific discovery in general and on the serendipity pattern in particular.

Here is a paper by Marlize Lombard & Miriam Noël Haidle that develops and applies a visualisation technique to describe the complex series of actions required for tasks such as making a fire, using a composite, stone-tipped spear and making and using a bow and arrow - three vital technologies for human history.

Above an example of the visualisation as applied to using a stone-tipped spear.

The Abstract reads:

For various reasons increased effort has recently been made to detect
the early use of mechanically-projected weaponry in the archaeological
record, but little effort has yet been made to investigate explicitly
what these tool sets could indicate about human cognitive evolution.
Based on recent evidence for the use of bow-and-arrow technology during
the Middle Stone Age in southern Africa by 64 kya, we use the method of
generating and analysing cognigrams and effective chains to explore
thought-and-action sequences associated with this technology. We show
that, when isolated, neither the production of a simple bow, nor that of
a stone-tipped arrow, can be reasonably interpreted to indicate tool
behaviour that is cognitively more complex than the composite artefacts
produced by Neanderthals or archaic modern Homo.
On the other hand, as soon as a bow-and-arrow set is used as an
effective group of tools, a novel cognitive development is expressed in
technological symbiosis, i.e. the ability to conceptualize a set of
separate, yet inter-dependent tools. Such complementary tool sets are
able to unleash new properties of a tool, inconceivable without the
active, simultaneous manipulation of another tool. Consequently,
flexibility regarding decision-making and taking action is amplified.
The archaeological evidence for such amplified conceptual and
technological modularization implies a range of cognitive and
behavioural complexity and flexibility that is basic to human behaviour
today.

For those who have not met SAM before,I wish to summarizeVERY BRIEFLYwhat his old acquaintancesmay already know,and then to tell to all of youMORE about him.In the first place,the name “SAM”was first derived fromScience, Art, Mathematics;but I now findthe following interpretationmuch more helpful:the “S” stands forOUR CONTACT WITH THE OUTSIDE WORLD;please note thatI do NOT saythat “S” represents “facts” or “reality”,forthe only knowledge we can have ofthe outside worldis through our own senses or“extended” senses —like microscopes and telescopes et alwhich help us to see better,or radios, etc., whichhelp us to hear soundswhich we would otherwisenot be aware of at all,and so on and so on.

But of coursethere may bemany, many more thingsin the worldwhich we do not yet perceiveeither directly through our sensesor with the aid ofour wonderful inventions.And so it would beQuite arrogantto speak as if we knewwhat the outside world “really” is.That is why I wish to give to “S”the more modest interpretationand emphasize thatit represents merelythat PART of the OUTSIDE worldwhich we are able to contact, —and therefore even “S” hasa “human” element in it.

Furthermore,a Scientist utilizes the SAM within him,for he must make“observations” (“S”),he must use his “intuition” (“A”)to help him formulatea good set of basic postUlates,from which his “reasoning powers” (“M”)will then help him toderive conclusionswhich in turn must again be“tested” (“S” again!) to seeif they are “correct”.

Perhaps you are thinking thatSAM and the Scientistare really one and the same,and that all I am doing isto recommend that we all becomeScientists!But you will soon see thatthis is not the case at all.For,in the first place,it too often happens, —alas and alack! —that when a Scientist isnot actually engaged in doinghis scientific work,he may “slip” and not usehis “S”, his “A”, and his “M”,so carefully,will bear watching,like the rest of us.

The medic and writer Lewis Thomas (1913-1993) called the MBL (Marine Biological Laboratory, Woods Hole, Massachusetts) “a paradigm, a human institution possessed of a life of its own,
self-regenerating, touched all around by human meddle but consistently
improved, embellished by it.”